Hi all, this is by design. According to VA-760-PMT, the form is "Individuals must submit all income tax payments electronically if any payment exceeds $1,500 or the sum of all payments is expected to exceed $6,000. This includes estimated, extension, and return payments." See the form here. 
If a return does not meet these criteria, ProSeries will generate the voucher. Otherwise, the option to electronically file will be automatically checked.